Alignments for a candidate for ald-dh-CoA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Klebsiella michiganensis M5al

Align acetaldehyde dehydrogenase; EC 1.2.1.10 (characterized)
to candidate BWI76_RS16905 BWI76_RS16905 acetaldehyde dehydrogenase (acetylating)

Query= CharProtDB::CH_002283
         (316 letters)



>FitnessBrowser__Koxy:BWI76_RS16905
          Length = 316

 Score =  552 bits (1422), Expect = e-162
 Identities = 286/316 (90%), Positives = 300/316 (94%)

Query: 1   MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI 60
           MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDP+SDGLARARRMGVATTHEGV 
Sbjct: 1   MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPESDGLARARRMGVATTHEGVG 60

Query: 61  GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN 120
           GLM M EFADID VFDATSAGAHVKNDAALREAKP IR+IDLTPAAIGPYCVPVVNLEAN
Sbjct: 61  GLMQMAEFADIDFVFDATSAGAHVKNDAALREAKPGIRVIDLTPAAIGPYCVPVVNLEAN 120

Query: 121 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR 180
           + + NVNMVTCGGQATIPMVAAVSRVA+VHYAEIIASIASKSAGPGTRANIDEFTETTS+
Sbjct: 121 LAEGNVNMVTCGGQATIPMVAAVSRVAKVHYAEIIASIASKSAGPGTRANIDEFTETTSQ 180

Query: 181 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY 240
           AIE VGGAAKGKAIIVLNPAEPPLMMRDTVYVLS+ ASQ DI ASI EMA AVQAYVPGY
Sbjct: 181 AIEKVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSEAASQQDIAASIAEMAAAVQAYVPGY 240

Query: 241 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT 300
           RLKQ+VQFEVIP+DKPVNLPGVG+FSGLKTAV+LEVEGAAHYLPAYAGNLDIMTS+ALAT
Sbjct: 241 RLKQQVQFEVIPEDKPVNLPGVGRFSGLKTAVYLEVEGAAHYLPAYAGNLDIMTSAALAT 300

Query: 301 AEKMAQSLARKAGEAA 316
           AEKMAQ++   AGEAA
Sbjct: 301 AEKMAQAMNDAAGEAA 316


Lambda     K      H
   0.317    0.132    0.368 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 406
Number of extensions: 5
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 316
Length of database: 316
Length adjustment: 27
Effective length of query: 289
Effective length of database: 289
Effective search space:    83521
Effective search space used:    83521
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS16905 BWI76_RS16905 (acetaldehyde dehydrogenase (acetylating))
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03215.hmm
# target sequence database:        /tmp/gapView.2670.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03215  [M=285]
Accession:   TIGR03215
Description: ac_ald_DH_ac: acetaldehyde dehydrogenase (acetylating)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.5e-144  466.6   8.5   1.7e-144  466.4   8.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS16905  BWI76_RS16905 acetaldehyde dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS16905  BWI76_RS16905 acetaldehyde dehydrogenase (acetylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.4   8.5  1.7e-144  1.7e-144       1     283 [.       3     308 ..       3     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: 466.4 bits;  conditional E-value: 1.7e-144
                               TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didi 67 
                                             k kvaiiGsGnigtdl+ik+lr +++le+a++vGidpesdGlarar++gv+t++eGv +l+++    did 
  lcl|FitnessBrowser__Koxy:BWI76_RS16905   3 KRKVAIIGSGNIGTDLMIKILRhGQHLEMAVMVGIDPESDGLARARRMGVATTHEGVGGLMQMAefaDIDF 73 
                                             679*******************99*************************************9988899*** PP

                               TIGR03215  68 vfdatsakahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavs 136
                                             vfdatsa ah++n+++l+e+  g++vidltPaa+Gpy+vP+vnle++l++ nvn+vtCgGqatiP+vaavs
  lcl|FitnessBrowser__Koxy:BWI76_RS16905  74 VFDATSAGAHVKNDAALREAkpGIRVIDLTPAAIGPYCVPVVNLEANLAEGNVNMVTCGGQATIPMVAAVS 144
                                             *****************998779************************************************ PP

                               TIGR03215 137 rvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalve 207
                                             rvakv+yaei+asiasksaGpgtranideftetts+a+e+vgGa+kgkaii+lnPaePpl+mrdtvy+l+e
  lcl|FitnessBrowser__Koxy:BWI76_RS16905 145 RVAKVHYAEIIASIASKSAGPGTRANIDEFTETTSQAIEKVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSE 215
                                             *********************************************************************** PP

                               TIGR03215 208 eadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGagdylPky 261
                                             +a++++i+as++em ++vq+yvpGyrlkq+v+++                 g k++v+leveGa++ylP+y
  lcl|FitnessBrowser__Koxy:BWI76_RS16905 216 AASQQDIAASIAEMAAAVQAYVPGYRLKQQVQFEvipedkpvnlpgvgrfsGLKTAVYLEVEGAAHYLPAY 286
                                             *********************************************************************** PP

                               TIGR03215 262 aGnldiltaaalavaeklaeel 283
                                             aGnldi+t+aala+aek+a+++
  lcl|FitnessBrowser__Koxy:BWI76_RS16905 287 AGNLDIMTSAALATAEKMAQAM 308
                                             *******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (316 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.96
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources